diff --git a/docs/pipelines/flexiprep.md b/docs/pipelines/flexiprep.md
index cd1e3f8400e9b9bcce0e03fa8ee335e812bb562c..2140398ab88dd7ae89d99b23e9539b2a4dd4ad44 100644
--- a/docs/pipelines/flexiprep.md
+++ b/docs/pipelines/flexiprep.md
@@ -44,8 +44,8 @@ Command line flags for Flexiprep are:
 
 | Flag  (short)| Flag (long) | Type | Function |
 | ------------ | ----------- | ---- | -------- |
-| -R1 | --input_r1 | Path (**required**) | Path to input fastq file |
-| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
+| -R1 | --inputR1 | Path (**required**) | Path to input fastq file |
+| -R2 | --inputR2 | Path (optional) | Path to second read pair fastq file. |
 | -sample | --sampleid | String (**required**) | Name of sample |
 | -library | --libid | String (**required**) | Name of library |
 
diff --git a/docs/pipelines/mapping.md b/docs/pipelines/mapping.md
index f04efebc60425764eeb38cbeae90ca9f4751865b..79d2a57494ca3fb24e369515dcfed47b883bf556 100644
--- a/docs/pipelines/mapping.md
+++ b/docs/pipelines/mapping.md
@@ -28,8 +28,8 @@ Command line flags for the mapping pipeline are:
 
 | Flag  (short)| Flag (long) | Type | Function |
 | ------------ | ----------- | ---- | -------- |
-| -R1 | --input_r1 | Path (**required**) | Path to input fastq file |
-| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
+| -R1 | --inputR1 | Path (**required**) | Path to input fastq file |
+| -R2 | --inputR2 | Path (optional) | Path to second read pair fastq file. |
 | -sample | --sampleid | String (**required**) | Name of sample |
 | -library | --libid | String (**required**) | Name of library |
 
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 134fd13be1fb5d57aa7c75e06c2c57ea509c666c..ab87244ee6329c0163d91660df6e8f57f866949a 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -27,10 +27,10 @@ import org.broadinstitute.gatk.queue.QScript
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
   def this() = this(null)
 
-  @Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", required = true)
+  @Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", fullName = "inputR1", required = true)
   var inputR1: File = _
 
-  @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
+  @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", fullName = "inputR2", required = false)
   var inputR2: Option[File] = None
 
   /** Skip Trim fastq files */
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index c6d192cf2d2084a4752d0b235eba6aefa2701eab..fa1494e6c6693d28df1fea45c053a09dee52937d 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -41,10 +41,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
   def this() = this(null)
 
-  @Input(doc = "R1 fastq file", shortName = "R1", required = true)
+  @Input(doc = "R1 fastq file", shortName = "R1", fullName = "inputR1", required = true)
   var inputR1: File = _
 
-  @Input(doc = "R2 fastq file", shortName = "R2", required = false)
+  @Input(doc = "R2 fastq file", shortName = "R2", fullName = "inputR2", required = false)
   var inputR2: Option[File] = None
 
   /** Output name */